Patients with ICF (Immunodeficiency, Centromeric instability, and Facial anomalies) syndrome suffer from recurrent and often fatal respiratory and gastrointestinal infections due to agammaglobulinemia with B cells as well as a variety of congenital malformations. In approximately half of the patients mutations in the DNA methyltransferase 3B (DNMT3B) gene have been identified as the underlying cause of ICF syndrome (ICF1), while in the remainder of patients the gene defect is unknown. These ICF2 patients without DNMT3B defect show a clinical phenotype identical to ICF1 patients. All patients with ICF, both ICF1 and ICF2, suffer from agammaglobulinemia with B cells. Upon phytohaemagglutinin stimulation, multiradiate chromosomes can be identified in all ICF patients. In addition, specific DNA repeats show pronounced hypomethylation. Both observations are considered molecular hallmarks for ICF syndrome. Since all ICF2 patients show alpha-satellite repeat hypomethylation, which distinguishes them from ICF1 patients, the involvement of a second disease locus (gene defect) in ICF2 syndrome is expected. This is further substantiated by the identification of three ICF2 cases in which the DNMT3B gene is excluded by genetic studies. The central premise of this application is to identify the gene defect and primary pathogenic mechanism underlying ICF2 syndrome. First, using the method of homozygosity mapping, candidate loci that show homozygosity by descent in five consanguineous ICF2 patients will be identified. Additional ICF2 cases are available to aid the mapping study. Second, by sequence determination of the whole human exome in two consanguineous ICF2 patients using the Illumina/Solexa Genome Analyzer, all homozygous DNA variants in these patients in all regions of homozygosity will be identified. Candidate genes carrying homozygous DNA variants will be prioritized for their causal involvement in ICF2 based on the absence of the identified sequence variants in SNP databases, gene function and codon change. Finally, by direct sequencing of all exons and exon-intron boundaries of the prioritized candidate genes in the remaining patients in combination with expression studies of the candidate genes in cell cultures of ICF2 patients, the gene defect underlying ICF2 syndrome will be identified. PUBLIC HEALTH RELEVANCE: The central premise of this application is to identify the gene defect in ICF2 syndrome, a primary immune deficiency. This will increase our understanding of the molecular mechanism underlying ICF2 syndrome, and may provide new clues for therapy. Additionally, it will improve prenatal and postnatal diagnosis of the disease and facilitate genetic counseling.